Working in these modes is going to be a pain in the arse whether you have a Windows GUI or not, the key with NUFLI is that you pixel unrestricted at C64 resoloution and in the C64 palette, then you let the converter work out all the boring stuff like sprite priorities. The editor then comes in use to fix any dodgy results, that's all! (unless you have a few spare years to do it all by hand :) )

When invoking 'palette setup' (CTRL+A), I get something like "Error 13: Type Mismatch". Doesn't this happen in Windows, too? I'd think so. BTW, it can be fixed in Palettes.ini by placing the closing ']' in line 204.